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The RNAscope® and BaseScope™ Assays are based on the proprietary RNAscope® Technology, enabling RNA target expression analysis within intact cells and tissues with high sensitivity and specificity.

RNAscope® Assay
The innovative RNAscope® Assay, with in situ hybridization technology to detect mRNA and ncRNA targets of >300bp, was launched in 2011 and marks the foundation of our product portfolio. The proprietary probe design requires an average of 20 Z pairs per target, however a minimum hybridization of 6 Z pairs can be used to obtain a signal. With over 800 publications in peer-reviewed journals, across multiple disciplines, the RNAscope® Assay represents a revolutionary advance in in situ target RNA detection.

BaseScope™ Assay
The BaseScope™ Assay is a recent addition to the RNAscope® Technology product portfolio, launched in early 2016. Using the same innovative technology and proprietary probe design as used in the RNAscope Assay, the BaseScope™ Assay is further refined to detect as few as 1-3 Z pairs. This powerful in situ hybridization technology enables the specific detection of exon junctions, short target/splice variants highly homologous sequences and point mutations, with single cell detection sensitivity in a broad range of tissues, samples and species.

RNAscope® and BaseScope™ Assay Comparison

comp rna scope


> More Information on RNAscope

> More Information on Base Scope 


RNAscope® Assay

BaseScope™ Assay

Number of ZZ Pair per target

Standard probe design is 20 ZZ probes (minimum of 6 ZZ probes)

1 to 3 ZZ probes based on the application


mRNA >300 bases
lncRNA > 300 bases

Exon junctions/Splice Variants
RNA 50 to 300 bases
Validated point mutations


lcnRNA and mRNA >300 bases

Exon junctions/splice variants, circular RNA, gene fusion, gene knockout
Short/highly homologous sequences, TCRs and CDR sequence for T cell clones, pre-miRNA, gene editing/CRISPR, CAR-T cell validation and detection
Point mutation, short InDel, homologues

Multiplex capability

Single to up to 12-plex

Single to Duplex


Chromogenic or fluorescent


Sample type

FFPE cells & tissues (TMAs)
Fresh frozen tissues
Fixed frozen tissues
Cultured cells

FFPE cells & tissues (TMAs)
Fresh frozen tissues
Fixed frozen tissues
Cultured cells

Pretreatment kit

Reagent Kit includes Universal Pretreatment Kit

Reagent kit includes Universal Pretreatment Kit


RNAscope® kit*

BaseScope™ kit*


RNAscope® probe*

BaseScope™ probe*


Available on Leica Bond Rx and Ventana Discovery ULTRA

Singleplex available on Leica Bond Rx and Ventana Discovery ULTRA


*RNAscope® and BaseScope™ Assay products components cannot be interchanged.